This document lists all of the objects in the data specification, and their fields. The NULL column indicates which objects can be empty (i.e. no value is provided). The column values indicates the possible values that this field can take.

Users are encouraged to contribute to the development of this data specification by suggesting improvements or changes online: https://github.com/mangal-wg/mangal-api/issues.

library(rmangal)
## Loading required package: igraph
## Loading required package: methods
## Loading required package: cheddar
options('width' = 150)
url = "http://localhost:8000/"
api = mangalapi(url)
print(api$resources)
## [1] "dataset"     "environment" "interaction" "item"        "network"     "reference"   "taxa"        "trait"       "user"

Node level

Taxa

kable(whatIs(api, 'taxa'), format="markdown")
field help type null unique values
1 bold The BOLD identifier of the taxa integer TRUE TRUE
2 description A short description of the taxa string TRUE FALSE
3 eol The EOL identifier of the taxa integer TRUE TRUE
4 gbif The GBIF identifier of the taxa integer TRUE TRUE
6 name The scientific name of the taxa string FALSE TRUE
7 ncbi The NCBI Taxonomy identifier of the taxa integer TRUE TRUE
9 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
10 status The taxonomic status of the taxa. string FALSE FALSE confirmed, trophic species, morphospecies, nomen dubium, nomen oblitum, nomen nudum, nomen novum, nomen conservandum, species inquirenda
11 traits A list of traits values indentifiers (or URIs) that were measured on this taxa. Good for taxa-level traits. related TRUE FALSE
12 tsn The TSN identifier integer TRUE TRUE
13 vernacular The vernacular name of the taxa, in English string TRUE FALSE

Population

kable(whatIs(api, 'population'), format="markdown")
## Error: This API do not implement objects of type population. See api$resources for more.

Item

kable(whatIs(api, 'item'), format="markdown")
field help type null unique values
1 description A short description of the population string TRUE FALSE
3 level Whether the item is a single individual, or a population string FALSE FALSE individual, population
4 name A name for the item, useful to identify it later string FALSE FALSE
6 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
7 size If the item is a population, the number of individuals or biomass float TRUE FALSE
8 taxa The identifier (or URI) of the taxa object to which the item belongs. related FALSE FALSE
9 traits A list of traits values indentifiers (or URIs) that were measured on this item. related TRUE FALSE
10 units Units in which the population size is measured string TRUE FALSE

Interaction level

Interaction

kable(whatIs(api, 'interaction'), format="markdown")
field help type null unique values
1 data List of identifiers (or URIs) of the references describing the data. related TRUE FALSE
2 date The time at which the interaction was sampled datetime TRUE FALSE
3 description A description of the interaction string TRUE FALSE
4 environment List of identifiers (or URIs) of the environments associated to the interaction. related TRUE FALSE
6 item_from Identifier (or URI) of the item establishing the interaction. related TRUE FALSE
7 item_to Identifier (or URI) of the item receiving the interaction. related TRUE FALSE
8 latitude Latitude string TRUE FALSE
9 link_type The type of interaction string FALSE FALSE predation, herbivory, ectoparasitism, endoparasitism, intra-cellular parasitism, parasitoidism, mycoheterotrophy, antixenosis, teletoxy, amensalism, antibiosis, allelopathy, competition, facilitation, refuge creation, inquilinism, phoresis, epibiosis, pollination, mutualistic symbiosis, zoochory, mutual protection
10 longitude Longitude string TRUE FALSE
11 obs_type How the interaction was observed string FALSE FALSE unspecified, observation, litterature, absence, inferred
13 papers List of identifiers (or URIs) of the references to the papers associated with the dataset. related TRUE FALSE
15 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
16 stage_from The stage of the establishing, to be selected in the list of allowed values string FALSE FALSE seed, juvenile, adult, dead, larva, all
17 stage_to The stage of the receiving entity, to be selected in the list of allowed values string FALSE FALSE seed, juvenile, adult, dead, larva, all
18 strength_f The strength of the interaction for the item ESTABLISHING the interaction float TRUE FALSE
19 strength_t The strength of the interaction for the item RECEVING the interaction float TRUE FALSE
20 taxa_from Identifier (or URI) of the taxa establishing the interaction. related FALSE FALSE
21 taxa_to Identifier (or URI) of the taxa receiving the interaction. related FALSE FALSE
22 units_f Units in which the interaction strength is measured string TRUE FALSE
23 units_t Units in which the interaction strength is measured string TRUE FALSE

Network

kable(whatIs(api, 'network'), format="markdown")
field help type null unique values
1 data List of identifiers (or URIs) of the references describing the data. related TRUE FALSE
2 date The time at which the network was sampled datetime TRUE FALSE
3 description A short description of the network string TRUE FALSE
4 environment List of identifiers (or URIs) of environmental measurements associated to the network. related TRUE FALSE
6 interactions List of identifiers (or URIs) of the interactions in the network. related FALSE FALSE
7 latitude Latitude string TRUE FALSE
8 longitude Longitude string TRUE FALSE
9 name The name of the network string FALSE FALSE
11 papers List of identifiers (or URIs) of the references to the papers associated with the dataset. related TRUE FALSE
13 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE

Dataset

kable(whatIs(api, 'dataset'), format="markdown")
field help type null unique values
1 data A list of the id of references for the data (e.g. data papers, figshare dataset) related TRUE FALSE
2 description A short description of the dataset string TRUE FALSE
3 environment List of identifiers (or URIs) of the environments associated to the dataset. related TRUE FALSE
5 name The name of the dataset string FALSE FALSE
6 networks A list of either the id of networks, or their representation in list format related FALSE FALSE
8 papers List of identifiers (or URIs) of the references to the papers associated with the dataset. related TRUE FALSE
10 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE

Meta-data

Trait value

kable(whatIs(api, 'trait'), format="markdown")
field help type null unique values
1 description A longer description of the trait string TRUE FALSE
3 name The name of the measured trait string FALSE FALSE
5 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
6 units Units in which the trait was measured string TRUE FALSE
7 value The value of the trait string FALSE FALSE

Environmental value

kable(whatIs(api, 'environment'), format="markdown")
field help type null unique values
1 description A description of the environmental property string TRUE FALSE
3 name The environmental property being measured string FALSE FALSE
5 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
6 units The units in which the environmental property is measured string TRUE FALSE
7 value The value of the environmental property string FALSE FALSE

Reference

kable(whatIs(api, 'reference'), format="markdown")
field help type null unique values
1 doi DOI of the reference object string TRUE FALSE
3 jstor JSTOR identifier of the reference object string TRUE FALSE
5 pmid PubMed ID of the reference object string TRUE FALSE
6 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
7 url URL of the reference object string TRUE FALSE

User

kable(whatIs(api, 'user'), format='markdown')
field help type null unique values
1 email Unicode string data. Ex: "Hello World" string FALSE FALSE
2 first_name Unicode string data. Ex: "Hello World" string FALSE FALSE
4 last_name Unicode string data. Ex: "Hello World" string FALSE FALSE
5 resource_uri Unicode string data. Ex: "Hello World" string FALSE FALSE
6 username Required. 30 characters or fewer. Letters, numbers and @/./+/-/_ characters string FALSE TRUE